Processing and analysis of new multichannel seismic records, coincident with wide-angle seismic profiles, acquired in the framework of the TsuJal project allow us to investigate in detail the complex structure of the oceanic domain in the collision zone between Rivera Plate and Block Jalisco at its northern termination. The subducting Rivera Plate, which is overridden by the North American Plate–Jalisco Block, is clearly identified up to 21.5°N (just south of Maria Magdalena Island) as a two clear reflections that we interpret as the interplate and Moho discontinuities. North of the Tres Marias Islands the seismic images display a different tectonic scenario with structures that are consistent with large faulting and rifted margin. A two-dimensional velocity approach for the crustal geometry is achieved using joint refraction/reflection travel time tomography, the uncertainty of the results is assessed by means of Monte Carlo analysis. Our results show an average oceanic crustal thickness of 6–7 km with a moderate increase towards the Jalisco Block, an anomalous thick layers (~3.0 km) displaying a relatively low velocity (~5.5 km/s) underneath Maria Magdalena Rise, and an estimated Moho depth deeper than 15 km in the collision zone between Rivera Plate and Jalisco Block. We have also determined an anomalous crust on the western flank of the Tres Marias Islands, which may be related to the initial phases of continental breakup of the Baja California Peninsula and Mexico mainland. High-resolution bathymetry provides remarkable images of intensive slope instabilities marked by relatively large slides scars of more than 40 km2 extent, and mass-wasting deposits probably triggered by the intense seismicity in the area.